Protective effect of Pien Tze Huang on colitis-associated colorectal cancer
RNA-seq (gene expression) · mouse · 20 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 20 samples: 5 × Colon, con vs 5 × Colon, PZH vs 5 × Colon, model vs 5 × Colon, MPZHGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Read the full summary ↓
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE230302_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA958214 and SRA study SRP433824. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 4 replicated groups read from 20 sample titles; they account for 20 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM7211473 Colon, con17 Colon, con
- GSM7211474 Colon, con37 Colon, con
- GSM7211475 Colon, con41 Colon, con
- GSM7211476 Colon, con48 Colon, con
- GSM7211477 Colon, con50 Colon, con
- GSM7211478 Colon, PZH8 Colon, PZH
- GSM7211479 Colon, PZH14 Colon, PZH
- GSM7211480 Colon, PZH27 Colon, PZH
- GSM7211481 Colon, PZH46 Colon, PZH
- GSM7211482 Colon, PZH53 Colon, PZH
- GSM7211483 Colon, model23 Colon, model
- GSM7211484 Colon, model30 Colon, model
- GSM7211485 Colon, model33 Colon, model
- GSM7211486 Colon, model44 Colon, model
- GSM7211487 Colon, model52 Colon, model
- GSM7211488 Colon, MPZH2 Colon, MPZH
- GSM7211489 Colon, MPZH13 Colon, MPZH
- GSM7211490 Colon, MPZH15 Colon, MPZH
- GSM7211491 Colon, MPZH35 Colon, MPZH
- GSM7211492 Colon, MPZH36 Colon, MPZH
- GSE265991 Pien Tze Huang enhances the killing effect of autologous T cells in colorectal cancer by inhibiting PD-L1, stem cell markers, and STAT3. 12 samples shares colorectal, huang, pien
- GSE268335 Transcriptome Analysis Reveals Potential Protective Effects and Biomarkers of Pien Tze Huang on CCl4-induced Liver Cancer (circRNA) 18 samples shares protective, huang, pien
- GSE269013 Transcriptomic analysis reveals the protective biomarkers of Pien Tze Huang in liver cirrhosis mice model [mRNA_lncRNA] 18 samples shares protective, huang, pien
- GSE223323 Enterocyte like differentiation defines metabolic gene signatures of CMS3 colorectal cancers and provides therapeutic vulnerability 148 samples shares colorectal
- GSE276018 Integrated Multi-Omics Analysis Reveals Epigenetic and Sex-Specific Alterations in Colorectal Cancer Cachexia 88 samples shares colorectal
- GSE306627 TGFβ signaling in cancer-associated fibroblasts drives a hepatic gp130-dependent pro-metastatic inflammatory program in colorectal cancer 42 samples shares colorectal
- GSE231804 IL-1R signaling drives enteric glia-macrophage interactions in colorectal cancer 39 samples shares colorectal
- GSE225104 RNA-Seq of gut of colorectal cancer mice fed black rice and control diets 38 samples shares colorectal
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.